It's one of the things that really pissed me off about the capture of the Citadel - you spend all this time there, helping people, building up relationships, friends and allies are there (Bailey, Kelly, Jacob, Aria), and there's absolutely no recognition of the fact that all of them are now dead, and all of that work was essentially worthless (although you could say that about a lot of the events in the trilogy - all for a couple of extra points on the War Assets chart...).

Actually, there's a relatively good chance that they're all still alive on the Citadel. The one thing everyone forgets is that the Illusive Man got himself super reaper-enhanced right before going to the citadel, apparently upgrading himself with a control signal that allows him to control both reaper forces and even human beings. TIM is indoctrinated, but he never DIRECTLY aides the reapers in combat.

It's more likely that the reapers let The Illusive Man think he was protecting the citadel by letting him maintain control of it and everyone on it with his little glowfist device (which means he probably put it under cerberus lockdown at the same time, kinda like he did on Omega and had earlier tried to do under Udina's watch). That would also explain why the citadel arms were closed when it arrived at Earth; the Protheans sabotaged the citadel so that it no longer responds to reaper commands, so they evidently used The Illusive Man just like they used Saren and got HIM to close the arms and lock the place down.

So everyone on the citadel is (or was) still alive when Shepard activated the crucible. Probably half to two thirds of them died when shep chose the destroy option, while about one third committed suicide as a result of the synthesis option. A smaller number -- Cerberus troops, mainly -- would have committed suicide after the control option, of course.